Current Protein Identity：P33755
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Difference tags compare only the current result set; every original PDB and assembly record remains separate.
Related-Structure Differences
Each row represents one biological assembly in one PDB entry; multiple monomers of the same protein are listed separately.
| PDB Entry | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Experimental Method | Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 6JWH Yeast Npl4 zinc finger, MPN and CTD domains Deposited 2019-04-20 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
113–580（468 aa）
|
Mutation：E123A,K124A,E125A | ZN ZINC ION × 2 GOL GLYCEROL × 9 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；4% Tacsimat (pH 6.0), 12% PEG 3350
|
Resolution 1.72 Å R-free 0.193 |
| 6JWI Yeast Npl4 in complex with Lys48-linked diubiquitin Deposited 2019-04-20 | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain A
113–580（468 aa）
|
Not recorded | ZN ZINC ION × 2 BCN BICINE × 5 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；100mM Bicine-NaOH (pH 6.5), 18% PEG 3350, 200mM lithium sulfate
|
Resolution 2.55 Å R-free 0.226 |
| 6JWI Yeast Npl4 in complex with Lys48-linked diubiquitin Deposited 2019-04-20 | Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain E
113–580（468 aa）
|
Not recorded | ZN ZINC ION × 2 BCN BICINE × 4 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；100mM Bicine-NaOH (pH 6.5), 18% PEG 3350, 200mM lithium sulfate
|
Resolution 2.55 Å R-free 0.226 |
| 6JWJ Npl4 in complex with Ufd1 Deposited 2019-04-20 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
113–580（468 aa）
|
Mutation：E123A,K124A,E125A | ZN ZINC ION × 2 GOL GLYCEROL × 11 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；90mM BisTris-HCl (pH 7.5), 19% PEG 3350, 10mM ATP
|
Resolution 1.58 Å R-free 0.206 |
| 6OA9 Cdc48-Npl4 complex processing poly-ubiquitinated substrate in the presence of ATP Deposited 2019-03-15 | Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric（10） Consistent with protein count |
Chain G
1–580（580 aa）
|
Not recorded | ATP ADENOSINE-5'-TRIPHOSPHATE × 9 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ZN ZINC ION × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE；Waited 20 seconds before blotting for 2.5-3 seconds.
|
Resolution 3.90 Å |
| 6OAA Cdc48-Npl4 complex processing poly-ubiquitinated substrate in the presence of ADP-BeFx, state 1 Deposited 2019-03-15 | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count |
Chain G
1–580（580 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 8 BEF BERYLLIUM TRIFLUORIDE ION × 6 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE；Waited 20 seconds before blotting for 2.5-3 seconds.
|
Resolution 4.10 Å |
| 8DAR Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex unbound but in the presence of SUMO-ubiquitin(K48polyUb)-mEOS and ATP Deposited 2022-06-14 | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric（8） Consistent with protein count |
Chain G
1–580（580 aa）
|
Not recorded | ATP ADENOSINE-5'-TRIPHOSPHATE × 6 ADP ADENOSINE-5'-DIPHOSPHATE × 6 ZN ZINC ION × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 8；20 mM HEPES pH 8.0, 150 mM NaCl, 0.1 mM TCEP, 1 mM MgCl2, 5 mM ATP. Added 0.05% CHAPSO before vitrification.
cryo-EM vitrification conditions
Cryogen ETHANE；8 s wait, 4 s blot before plunging
|
Resolution 3.00 Å |
| 8DAS Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex bound to two ubiquitin moieties in presence of SUMO-ubiquitin(K48polyUb)-mEOS and ATP, state 1 (intA) Deposited 2022-06-14 | Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric（10） Consistent with protein count |
Chain G
1–580（580 aa）
|
Not recorded | ATP ADENOSINE-5'-TRIPHOSPHATE × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 7 ZN ZINC ION × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 8；20 mM HEPES pH 8.0, 150 mM NaCl, 0.1 mM TCEP, 1 mM MgCl2, 5 mM ATP. Added 0.05% CHAPSO before vitrification.
cryo-EM vitrification conditions
Cryogen ETHANE；8 s wait, 4 s blot before plunging
|
Resolution 3.50 Å |
| 8DAT Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex bound to three ubiquitin moieties in presence of SUMO-ubiquitin(K48polyUb)-mEOS and ATP, state 1 (intB) Deposited 2022-06-14 | Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric（11） Consistent with protein count |
Chain G
1–580（580 aa）
|
Not recorded | ATP ADENOSINE-5'-TRIPHOSPHATE × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 7 ZN ZINC ION × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 8；20 mM HEPES pH 8.0, 150 mM NaCl, 0.1 mM TCEP, 1 mM MgCl2, 5 mM ATP. Added 0.05% CHAPSO before vitrification.
cryo-EM vitrification conditions
Cryogen ETHANE；8 s wait, 4 s blot before plunging
|
Resolution 3.80 Å |
| 8DAU Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex bound to two folded ubiquitin moieties and one unfolded ubiquitin in presence of SUMO-ubiquitin(K48polyUb)-mEOS and ATP, state 1 (uA) Deposited 2022-06-14 | Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric（11） Consistent with protein count |
Chain G
1–580（580 aa）
|
Not recorded | ATP ADENOSINE-5'-TRIPHOSPHATE × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 7 ZN ZINC ION × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 8；20 mM HEPES pH 8.0, 150 mM NaCl, 0.1 mM TCEP, 1 mM MgCl2, 5 mM ATP. Added 0.05% CHAPSO before vitrification.
cryo-EM vitrification conditions
Cryogen ETHANE；8 s wait, 4 s blot before plunging
|
Resolution 3.70 Å |
| 8DAV Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex bound to two ubiquitin moieties and one unfolded ubiquitin in presence of SUMO-ubiquitin(K48polyUb)-mEOS and ATP, state 2 (uC) Deposited 2022-06-14 | Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric（11） Consistent with protein count |
Chain G
1–580（580 aa）
|
Not recorded | ATP ADENOSINE-5'-TRIPHOSPHATE × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 7 ZN ZINC ION × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 8；20 mM HEPES pH 8.0, 150 mM NaCl, 0.1 mM TCEP, 1 mM MgCl2, 5 mM ATP. Added 0.05% CHAPSO before vitrification.
cryo-EM vitrification conditions
Cryogen ETHANE；8 s wait, 4 s blot before plunging
|
Resolution 3.50 Å |
| 8DAW Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex bound to three ubiquitin moieties and one unfolded ubiquitin in presence of SUMO-ubiquitin(K48polyUb)-mEOS and ATP, state 2 (uD) Deposited 2022-06-14 | Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric（12） Consistent with protein count |
Chain G
1–580（580 aa）
|
Not recorded | ATP ADENOSINE-5'-TRIPHOSPHATE × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 7 ZN ZINC ION × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 8；20 mM HEPES pH 8.0, 150 mM NaCl, 0.1 mM TCEP, 1 mM MgCl2, 5 mM ATP. Added 0.05% CHAPSO before vitrification.
cryo-EM vitrification conditions
Cryogen ETHANE；8 s wait, 4 s blot before plunging
|
Resolution 3.60 Å |
| 9OFV Consensus reconstruction of the eukaryotic Ribosome-associated Quality Control complex Deposited 2025-04-30 | Assembly 1 Protein–RNA Heteromer；Protein × 59 PDB declaration: 64-meric（64） Consistent with all polymers |
Chain G
1–580（580 aa）
|
Not recorded | ATP ADENOSINE-5'-TRIPHOSPHATE × 9 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ZN ZINC ION × 7 MG MAGNESIUM ION × 12 SPD SPERMIDINE × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.16 Å |